Get the Whitepaper called Using UPX as a Security Packer. It goes into detail on how to use this tool and how to bring obfuscation into it.
You can download it from the following link: https://packetstormsecurity.com/files/download/111072/Using_UPX_as_a_security_packer.pdf
Source: https://packetstormsecurity.com/files/111072/Using-UPX-As-A-Security-Packer.html